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Sodium in PDB 3f5m: Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei

Enzymatic activity of Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei

All present enzymatic activity of Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei:
2.7.1.11;

Protein crystallography data

The structure of Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei, PDB code: 3f5m was solved by I.W.Mcnae, J.Martinez-Oyanedel, J.W.Keillor, P.A.M.Michels, L.A.Fothergill-Gilmore, M.D.Walkinshaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.88 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 96.578, 117.570, 176.587, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 28.6

Other elements in 3f5m:

The structure of Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei (pdb code 3f5m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei, PDB code: 3f5m:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3f5m

Go back to Sodium Binding Sites List in 3f5m
Sodium binding site 1 out of 4 in the Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na489

b:30.6
occ:1.00
 OG1 A:THR451 2.7 13.3 1.0
OD2 A:ASP453 2.7 40.4 1.0
O A:VAL452 2.9 24.0 1.0
O A:ARG448 3.1 31.4 1.0
CA A:ARG448 3.4 20.1 1.0
CG A:ASP453 3.7 42.6 1.0
O A:THR451 3.7 19.6 1.0
C A:ARG448 3.7 23.1 1.0
C3 A:GOL488 3.8 35.0 1.0
C A:VAL452 3.9 21.0 1.0
C2 A:GOL488 3.9 41.1 1.0
CB A:THR451 3.9 23.3 1.0
CB A:ARG448 3.9 19.2 1.0
C1 A:GOL488 4.0 19.5 1.0
C A:THR451 4.1 20.8 1.0
CA A:ASP453 4.1 25.7 1.0
CB A:ASP453 4.3 23.7 1.0
N A:ASP453 4.4 20.1 1.0
O A:VAL447 4.4 26.6 1.0
O3 A:GOL488 4.5 26.5 1.0
CA A:THR451 4.5 20.9 1.0
OD1 A:ASP453 4.5 37.9 1.0
N A:ARG448 4.6 19.6 1.0
O1 A:GOL488 4.6 5.9 1.0
CG A:ARG448 4.6 22.6 1.0
N A:VAL452 4.8 14.3 1.0
N A:THR451 4.9 17.6 1.0
C A:VAL447 4.9 22.4 1.0
CA A:VAL452 5.0 22.8 1.0

Sodium binding site 2 out of 4 in 3f5m

Go back to Sodium Binding Sites List in 3f5m
Sodium binding site 2 out of 4 in the Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na490

b:43.0
occ:1.00
 OG A:SER318 2.6 19.9 1.0
O A:ALA262 2.9 46.2 1.0
O A:VAL260 3.1 18.9 1.0
O A:ARG317 3.1 28.2 1.0
O A:ALA259 3.3 23.3 1.0
C A:VAL260 3.5 16.2 1.0
CB A:ARG317 3.6 24.7 1.0
C A:ARG317 3.6 21.6 1.0
CA A:VAL260 3.6 17.4 1.0
O A:HOH496 3.6 15.2 1.0
C A:ALA262 3.7 23.8 1.0
CZ D:PHE137 3.8 26.0 1.0
CE1 D:PHE137 3.8 27.2 1.0
CB A:SER318 4.0 17.7 1.0
N A:ALA262 4.1 17.6 1.0
CA A:ARG317 4.2 25.2 1.0
C A:ALA259 4.2 24.9 1.0
N A:SER318 4.2 25.1 1.0
N A:VAL260 4.4 14.1 1.0
N A:ASN263 4.4 24.1 1.0
CA A:SER318 4.4 22.8 1.0
N A:SER261 4.5 17.0 1.0
CA A:ASN263 4.5 28.7 1.0
CA A:ALA262 4.6 13.6 1.0
CB A:VAL260 4.8 13.9 1.0
O A:HOH513 4.8 31.0 1.0
CG1 A:VAL260 4.8 30.5 1.0
CG A:ARG317 4.8 26.3 1.0
N A:TYR264 4.9 25.0 1.0
C A:SER261 5.0 26.6 1.0
CD A:ARG317 5.0 27.2 1.0

Sodium binding site 3 out of 4 in 3f5m

Go back to Sodium Binding Sites List in 3f5m
Sodium binding site 3 out of 4 in the Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na488

b:45.9
occ:1.00
 OG B:SER318 3.0 32.5 1.0
O B:VAL260 3.1 27.8 1.0
O B:HOH561 3.5 40.8 1.0
CB B:ARG317 3.5 23.9 1.0
O B:ALA262 3.6 35.4 1.0
C B:VAL260 3.7 21.6 1.0
CZ C:PHE137 3.7 23.8 1.0
O C:HOH553 3.7 18.7 1.0
O B:ARG317 3.8 31.4 1.0
CA B:VAL260 3.8 20.8 1.0
CE1 C:PHE137 4.0 25.8 1.0
C B:ARG317 4.0 25.1 1.0
O B:ALA259 4.0 24.3 1.0
C B:ALA262 4.3 29.8 1.0
CA B:ARG317 4.3 29.2 1.0
NH2 C:ARG136 4.4 32.8 1.0
CB B:SER318 4.4 21.8 1.0
CG1 B:VAL260 4.6 30.1 1.0
N B:SER318 4.6 33.6 1.0
CD B:ARG317 4.6 43.6 1.0
CG B:ARG317 4.7 33.1 1.0
N B:ALA262 4.7 23.1 1.0
N B:SER261 4.8 20.6 1.0
CB B:VAL260 4.8 22.1 1.0
N B:VAL260 4.8 15.4 1.0
C B:ALA259 4.9 25.9 1.0
N B:ASN263 4.9 29.3 1.0
CA B:ASN263 4.9 30.6 1.0
CE2 C:PHE137 5.0 22.3 1.0
CA B:SER318 5.0 25.4 1.0

Sodium binding site 4 out of 4 in 3f5m

Go back to Sodium Binding Sites List in 3f5m
Sodium binding site 4 out of 4 in the Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na490

b:34.6
occ:1.00
 OD2 C:ASP453 2.7 46.8 1.0
OG1 C:THR451 2.9 17.9 1.0
O C:VAL452 3.0 20.3 1.0
O C:ARG448 3.2 29.7 1.0
CA C:ARG448 3.5 20.3 1.0
CG C:ASP453 3.7 39.4 1.0
C3 C:GOL488 3.7 17.3 1.0
C C:ARG448 3.8 22.3 1.0
O C:THR451 3.8 19.8 1.0
C C:VAL452 3.9 23.2 1.0
CB C:ARG448 4.0 18.2 1.0
O3 C:GOL488 4.0 9.0 1.0
CA C:ASP453 4.1 27.3 1.0
O C:HOH549 4.1 23.5 1.0
CB C:THR451 4.1 23.7 1.0
C C:THR451 4.2 20.7 1.0
CB C:ASP453 4.3 18.5 1.0
N C:ASP453 4.4 24.5 1.0
OD1 C:ASP453 4.5 41.4 1.0
CG C:ARG448 4.6 19.3 1.0
O C:VAL447 4.6 21.3 1.0
N C:ARG448 4.7 16.2 1.0
CA C:THR451 4.7 19.1 1.0
C2 C:GOL488 4.9 28.4 1.0
O2 C:GOL488 4.9 11.4 1.0
N C:VAL452 4.9 14.2 1.0

Reference:

I.W.Mcnae, J.Martinez-Oyanedel, J.W.Keillor, P.A.Michels, L.A.Fothergill-Gilmore, M.D.Walkinshaw. The Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei Reveals Conformational Transitions Different From Those of Other Phosphofructokinases. J.Mol.Biol. V. 385 1519 2009.
ISSN: ISSN 0022-2836
PubMed: 19084537
DOI: 10.1016/J.JMB.2008.11.047
Page generated: Mon Oct 7 08:57:56 2024

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